Cleanup and documentation!
ramp: New class for polynomial ramps. Instantiated in the ForwardModel.
forwardmodel: Now uses new ramp class.
phasemapper: Ramp functionality moved to ramp class.
reconstruction: Ramp order not used, ramp can be now retrieved from the ramp
                class after reconstruction.
analytic, magcreator: Better and consistent definition of pixel centers and
                      their influence on the phase.
testing: Minor corrections for new syntax.

colormap: New module with colormap subclass which has special functions to
          calculate directional rgb-colors, now used in many plots!
__init__: On star import now also has abbreviations for a few modules.
fwd_model: Now has flags for fitting an offset and/or ramp.
           CAUTION: will be moved next update to new class!
magdata: Removed colorwheel stuff (all moved to 'colormap'). Overhaul of quiver
         plot in 2D and 3D. Now shows mask and uses new colormap for angular
         color coding.
phasemap: Now uses the new colormap for holo plots. Removed color wheel (moved
          to the new class). Added function to add ramps.
phasemapper: Now handles also offsets and ramps in the phase.
             CAUTION: will be moved next update to new class!
projector: Fixed bugs in SimpleProjector. 1) leftmost pixels are no longer moved
           moved to left corner of padded projection (when dim_uv is not None).
           2) odd padding when using dim_uv are now handled properly (one more
           pixel on top and right if necessary).
costfunction: n is now taken from the fwd_model instead of the data_set.
dataset: Introduced the count variable which gives the number of images.
magcreator: In the process of updating, more on next commit.
reconstruction: Also handles ramps and offsets now, properly extracts them after
                reconstruction.
regularisator: New argument 'add_params' is used to cut off input (for offset
               and ramp) which are not used in the regularisation.
scripts: several small changes...

Phase maps now also have a mask and a confidence matrix.
Began new script structure (temporary folders created).
Cleanup, logging and documentation done.
config: NTHREADS is now set here.
dataset: Method for creating 3D masks added.
phasemap: Mask and confidence matrix added. Padding and cropping supported.
forwardmodel: Stubs for multiprocessing added (next TODO!).
kernel: Added support for perturbed reference wave.
magdata: Padding and cropping supported.
projector: New property 'sparsity' introduced.
regularisator: Stub for ComboRegularisator added (next TODO!).
tests: Changed accordingly.

tests: implemented the missing TestCases!
dataset: mask is now created if not given!
phasemapper: guaranteed np.float32 format for RDRC (expected by Cython)
projector: now uses fft.FLOAT

docstrings: updated!
costfunction: CFAdapterScipyCG obsolete, deleted estimate_lambda()
dataset: use_fftw and threads obsolete
diagnostics: implemented stuff... much stuff...
fft: Docstrings and implementation of threads
magcreator: fixed bug in slab (dimension mix-up)
phasemap: plot now also returns colorbar
reconstruction: PrintIterator and optimize_simple_leastsq obsolete
regularisator: Docstrings
scripts: minor modifications
scripts - reconstruct_random_pixels: now use optimize_linear
testcases: analytic, compliance, kernel, magcreator, magdata, projector

kernel, phasemapper: now use the new pyramid.fft module.
MagData, PhaseMap: now use np.float32 instead of np.float64
MagData: new quiver_plot3d with just matplotlib (buggy and still WOP).
logging: deleted several logging.debug prompts for speed up.
util: deleted module!

Se_inv: is now handled differently, defaults to eye-matrix, but can be set
        later (added a few convenience functions to DataSet)
utility: (re-)added utility module for index conversion
kernel/phasemapper: can now use FFTW library and operate on pre-allocated
        arrays
dtype: set dtype of arrays to np.float32/np.complex64 (halves memory size),
       also applied to numcore routines!
magdata: quiver_plot can now plot every n-th arrow (yet untested!)
reconstruction scripts: modified several reconstruction scripts.

setup: Changes to setup.py, pyramid.version to fit to numpy and jutil
       now uses __all__ magic and supports from pyramid import *
tests: changes to test_compliance/magcreator/analytic (should now work)
collaborations: added several scripts for Patrick
reconstruction: added batch file for the reconstruction of several configs
test methods: (unfinished) scripts for fftw tests and kernel comparisons
paper 1: ch5-4 changed padding values to 0, 1, 3 and 7
plotting: deleted plt.show() lines (have to be done manually now or via Spyder)
logging: now named _log instead of LOG (private variable instead of constant)
         also some logs were disabled, because Pylint says they are slow...
reconstruction: now has info argument (pass a list in which cost info is copied)
phasemapper: changed sign of constant PHI_0, is now correctly positive (instead
             the negative z-integration is taken into account which was not done
             before!)
kernel: now uses FFTW, numpy code was changed accordingly and is still available
phasemapper: also uses FFTW now, work in progress: FFTW for jac_T_dot

        m: i'm'age
        n: i'n'put

Still to do: PhaseMapperElectric does not work
             3D reconstruction does not converge

minor changes to plotting methods (PhaseMap now plottable without colorbar).
phase_map: gain can now be set to 'auto' (5 fringes, determined by max. phase).
renamed 'density' to 'gain' (makes more sense).
regularisator: started to include norms and more kinds of regularisations.
mag_slicer: GUI which can go through loaded magnetizations along the major axes.
paper 1: minor changes to the scripts for the results.

magdata: implemented save_to_x3d (Bielefeld collaboration)
template.x3d: template for the x3d output (header file with spin-blueprints)
numcore.kernel_core: implemented multiply_jacobi_T_core
scripts: added vtk scripts for full nanowires and segments
         script to process file by Daniel Rüffner

pep8: optimizations
phasemapper_core: numcore module for phasemapper
scripts: compatibility with new structure
reconstruction: new scripts

package: some minor corrections (mainly import statements), some old functions
         were revived (e.g. in MagData)

scripts: adaption to the new structure and sorting (more work is to do here...)

_version: __version__ string is now imported from this file

phasemapper_core.pyx: added to separate the corresponding numcore_functions
                      from kernel_core.pyx

Renames:
datacollection --> dataset
optimizer      --> reconstruction

scripts:
interactive_setup is now implemented in an extended Spyder startup file.
some other scripts are now
the rest is NOT adapted, yet, which is the next task at hand
furthermore scripts will be sorted and unused ones deleted in the next commit

not represent the correct matrizes (hopefully, now they do).

>>> PACKAGE
forwardmodel, kernel, phasemapper:
        b_0 is now again inherent part of the kernel.
projector:
        Corrected .jac_T_dot, now delivers product for the correct matrix.
>>> SCRIPTS
simple_reconstruction:
        Does simple compliance tests for 1 and 2 projections and tests a simple
        solver via scipy.sparse.linalg.cg for the reconstruction.

documentation: minor changes and updates of docstrings

regrid: Added many scripts for regridding by Jörn
logging: Introduced logging
scripts: Added Scripts for regridding and simulating stuff for cooperations
removed: Unused test scripts
structure: Many new restructuring aspects already implemented

modularity and compatibility with future algorithms and ideas.

(At the moment a bit slow, optimization with Cython seems necessary).

Replaced res with a for the grid spacing
(resolution is a reserved word in electron microscopy
Work in progress: jacobi matrix for projection

phasemapper: added Kernel helper class with methods to calculate the jacobi
matrix or to multiply a vector with the (transposed) jacobi matrix without
explicitly calculating the full matrix
magcreator: added Shape.ellipsoid
numcore: added (experimental) speed-up for jacobi-matrix (not faster)
scripts: modified get_jacobi to test the new Kernel class,
tests: test_compliance now also searches and creates a list of TODOs

phasemapper: new function get_kernel() for convenience, mag_real_fast() for
calculation of the phase with pre-computed lookup-tables
projector: single_tilt_projection() now works as intended
Added scripts for the creation of core-shell-structures
Added script for charge calculation by contour integration
Added script for creating tilt series of core-shell-structure for reconstruction
Various minor modifications, mostly nomenclature and streamlining

pyramid: all docstrings in numpydoc (package installed) format (used by spinx)
holoimage: removed error, phase was falsely multiplied by pi/2
magcreator: removed create_mag_dist_comb, renamed functions for disc and vortex
magdata: Allows creation of empty MagData objects and easy adding of magnitudes
phasemap: Allows units to be set for plots, added 3D plot
phasemapper: Electrostatic component implemented
projector: Projection now includes thickness profile
docs: support for html, latex and pdf (experimental), use "make *" in shell
scripts: new structure, deleted some compare_* functions, added test_methods
.hpignore: now also ignores *.c and _* files (_build used in docs)

holoimage: changed colorwheel (now without axes)
magcreator: create_vortex now also allows a 3D-center (2D is extracted)
magdata: new methods: get_mask() and scale_down()
phasemap: changed plotting defaults (new kwargs)
phasemapper: started on electrical contribution

numcore: deleted c1, c2, c3, name changes in phase_mag_real
analytic: name change beta to phi
phasemapper: changes to include numcore
test_compliance: also checkes .pyx files now
setup: now works properly (hopefully on other systems, too)
compare_discs: added script to compare discs

scripts: changed scripts to work with the new syntax of the package
PhaseMag and MagData: added load and save options for NetCDF files
MagData: changed 3D-plotting to use mayavi (faster and better looking)
test: added more TestCases for various modules
phasemapper: added computation method to use mx and my (now standard)
compare_method_errors: first draft of script to compare the different errors

Scripts are nearly adapted to the new structure and easier to read.
(Except analytic module and scripts get_jacobi and inverse)

For Pushing Purposes

Changed setup.py
Implemented assertion to check if jacobi matrix is the same

test: changed the dataloader TestCase
pyramex: first experiments with Cython and SCons
dataloader: changed the order in which the dimensions are saved,
        z_len is no longer part of the magnetization (this was the reason why
        we had to divide by res, which is equal to z_len for calculating coeff)
magcreator: shapes are now separate functions, mag_shape is now an argument for
        one unified create_hom_mag-function
phasemap: unification of the phasemap-functions in real space (just the pixel-
        field is calculated different now)